Showing : genomicfeatures • reset
2
votes
3
replies
379
views
Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures Guitar txdbmaker GenomicRanges
written 15 days ago by ▴ 10
4
votes
9
replies
3.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 11 months ago by ★ 3.4k • written 13 months ago by ▴ 20
0
votes
3
replies
718
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures
14 months ago • updated 13 months ago rania.alanany • 0
3
votes
3
replies
870
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
15 months ago • updated 13 months ago mat149 ▴ 80
0
votes
2
replies
1.1k
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
written 23 months ago by ▴ 10
2
votes
1
reply
1.5k
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
1
reply
1.4k
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.2 years ago rohitsatyam102 ▴ 20
2
votes
3
replies
5.1k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
votes
2
replies
1.2k
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
2.4 years ago Geert ▴ 10
0
votes
2
replies
2.0k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.6 years ago gernophil • 0
1
vote
4
replies
1.4k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
vote
0
replies
952
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
2.7 years ago Shreyash ▴ 10
4
votes
8
replies
3.2k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
2.8 years ago davidhillis • 0
0
votes
2
replies
1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.0 years ago by • 0
0
votes
5
replies
2.0k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
918
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.2 years ago nattzy94 ▴ 20
0
votes
2
replies
1.9k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
4
replies
3.1k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
5
votes
9
replies
2.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.4 years ago by 43k • written 3.8 years ago by • 0
0
votes
18
replies
5.9k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.9 years ago rbenel ▴ 50
3
votes
3
replies
2.2k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3.7 years ago by 68k • written 4.1 years ago by ▴ 30
1
vote
2
replies
2.1k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
votes
3
replies
4.0k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
votes
2
replies
1.4k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
5
votes
2
replies
1.7k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.3 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.8k
views
install GenomicFeatures fail
GenomicFeatures install
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 80
1
vote
4
replies
2.3k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
4.4 years ago A.J. ▴ 20
1
vote
3
replies
1.8k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
4.4 years ago A.J. ▴ 20
1
vote
0
replies
1.7k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.3k
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
4.7 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
5
replies
3.9k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.8 years ago sieminsk • 0
2
votes
2
replies
2.3k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.9 years ago erhoppe • 0
0
votes
6
replies
2.0k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.9 years ago rproendo ▴ 30
0
votes
3
replies
1.7k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.2 years ago by • 0 • written 5.2 years ago by ▴ 120
0
votes
2
replies
4.4k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
votes
1
reply
1.1k
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.9 years ago by ▴ 80 • written 5.3 years ago by ▴ 10
0
votes
1
reply
6.0k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 90
3
votes
7
replies
2.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
0
votes
1
reply
1.8k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.5 years ago by 4.3k • written 5.5 years ago by • 0
3
votes
6
replies
3.3k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 120
0
votes
1
reply
1.9k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 100
0
votes
2
replies
1.6k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 10
0
votes
0
replies
1.4k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.7 years ago Guandong Shang ▴ 40
0
votes
2
replies
1.2k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 40
2
votes
3
replies
2.5k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 100
3
votes
4
replies
1.7k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 40
1
vote
2
replies
1.4k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.9 years ago by 4.3k • written 5.9 years ago by • 0
0
votes
2
replies
1.4k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
292 results • Page 1 of 6
Recent ...
Replies
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: > Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequences.…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Locations • All
United States, 19 minutes ago
United States, 27 minutes ago
United States, 40 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 921 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6